Hybrid economy, specialist cities can double as production, cottage cities bring in the moneys.
Also, a good portion of city sites can really only run one or the other. IE if you have a ton of grassland and 0 - 1 food resources... running specialists is kinda wasteful. On the other hand, if you have a city with 3 fish and only access to 3 plains or something, running specalists is only logical.
Typically, Ill have 3 specialist cities, 1 main big one with a ne, and then 2 support gp farms that sort of double as production cities. This is my ideal number at least, but sometimes city sites sort of force me into having more or less
I like Elizabeth for difficulties below Immortal, but thats only because I like to see ridiculous numbers on the science chart in the middle ages. For Immortal+, financial/philisophical combo just doesnt have enough strength early on to be the best pick.